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Assign snps to clumps based on LD after gwas

Source: R/snp_make_clumps.R
snp_make_clumps.Rd

Assign snps to clumps based on LD after gwas

Usage

snp_make_clumps(
  geno.bed.filename,
  geno.bed.dir,
  gwas.res,
  pvals.in.log = T,
  window = 500,
  ld.thresh = 0.5,
  plink.path = NULL,
  out.dir = NULL
)

Arguments

geno.bed.filename

character, filename of genotype bedfile, no .bed extension

geno.bed.dir

character, path to directory where bed/bim/fam files exist, include trailing "/"

gwas.res

data.frame, table of gwas results with columns (marker.ID, CHR, POS, PVAL)

pvals.in.log

boolean, are pvalues in gwas.res in -log10(p) or not

window

integer, window in kilobases either side of snp to look for snps in LD,

ld.thresh

numeric, R2 threshold above which snps will be grouped

path to plink 2 executable

out.dir

character, path to a temporary directory to output some intermediate files

Value

table with columns marker.ID and clump_num. Clump_num indicates groupings, numberings start from the larges pvalue to smallest. May want to reassign afterwards to be along the genome.

Examples

tag.snp <- "Chr_05-6857045"
gwas.df <- read.csv(system.file(
    "extdata",
    "PanvarExample_GLM_GWASresults.csv",
    package = "panvaR"))
annotation.table <- read.csv(system.file(
    "extdata",
    "Setaria_shattering_annotation.csv",
    package = "panvaR"))
plink.path <- bigsnpr::download_plink2()
temp.dir <- file.path(tempdir(), "panvar_ex")
dir.create(temp.dir, showWarnings = FALSE)
geno.bed.filename <- "Setaria_shattering_example_pruned.bed"
geno.bed.directory <- system.file("extdata", package="panvaR")

# look at only significant snps 
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
gwas.df_sub <- gwas.df %>% 
  filter(LOGPVAL > 8)

# get clumps
clump.table <- snp_make_clumps(
  geno.bed.filename = geno.bed.filename,
  geno.bed.dir = geno.bed.directory,
  gwas.res = gwas.df_sub,
  pvals.in.log = FALSE,
  window = 500,
  ld.thresh = .5,
  plink.path = plink.path,
  out.dir = temp.dir)
#> Markers in the following form in bed file: Chr_05-6357123
#> Creating clumps...
#> 
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 head(clump.table)
#>        marker.ID clump_num
#> 1 Chr_05-6419601         1
#> 2 Chr_05-6463617         1
#> 3 Chr_05-6466490         1
#> 4 Chr_05-6467430         1
#> 5 Chr_05-6474403         1
#> 6 Chr_05-6474887         1

# clean up
unlink(temp.dir, recursive = TRUE)